I really wouldn't know, other than stuff you could change in the current game. (expand the doff system, more minor factions, pvp rewards, more planets to visit, ground combat revamp etc...)
Most of the things that would come to mind, would probably kill the game within a few months. For example if the game were to use a high-end graphics engine, it would sure look nice ony my machine, but it would cut off customers with average or below-average computers, whose numbers are usually rather high in an mmo.
Reintroducing a sub-only model didn't work out financially, so it'd have to be a F2P model, which would have to include some means of money generation, e.g. lockboxes or the likes.
1. Address the balance issues I keep hearing about, re: make cruisers less gimped.
2. Add Romulans, Cardassians, and/or POSSIBLY the Dominion as playable factions.
3. Make the storyline missions less redundant! I keep find myself playing the same formula of "space combat, followed by ground combat, followed by yet more space combat." I'd like to see more missions that have an emphasis on problem-solving, or science, or diplomacy or ethical dilemmas. Basically, I'd like the game to reflect what makes Star Trek great, and that is transposing real world issues/dilemmas/philosophical questions into a sci fi setting. Don't get me wrong, space/ground combat is nice, but I don't think it should be the totality of the game.